[2024-01-25 18:02:35,544] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:35,545] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:35,545] [INFO] DQC Reference Directory: /var/lib/cwl/stgf525099e-940c-478b-8608-d6af1fe294a4/dqc_reference
[2024-01-25 18:02:36,752] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:36,753] [INFO] Task started: Prodigal
[2024-01-25 18:02:36,753] [INFO] Running command: gunzip -c /var/lib/cwl/stg454b5f82-57bf-4eba-b86c-a519988e64e9/GCF_022870865.1_ASM2287086v1_genomic.fna.gz | prodigal -d GCF_022870865.1_ASM2287086v1_genomic.fna/cds.fna -a GCF_022870865.1_ASM2287086v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:46,071] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:46,072] [INFO] Task started: HMMsearch
[2024-01-25 18:02:46,072] [INFO] Running command: hmmsearch --tblout GCF_022870865.1_ASM2287086v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf525099e-940c-478b-8608-d6af1fe294a4/dqc_reference/reference_markers.hmm GCF_022870865.1_ASM2287086v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:46,270] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:46,271] [INFO] Found 6/6 markers.
[2024-01-25 18:02:46,293] [INFO] Query marker FASTA was written to GCF_022870865.1_ASM2287086v1_genomic.fna/markers.fasta
[2024-01-25 18:02:46,293] [INFO] Task started: Blastn
[2024-01-25 18:02:46,293] [INFO] Running command: blastn -query GCF_022870865.1_ASM2287086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf525099e-940c-478b-8608-d6af1fe294a4/dqc_reference/reference_markers.fasta -out GCF_022870865.1_ASM2287086v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:47,020] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:47,024] [INFO] Selected 13 target genomes.
[2024-01-25 18:02:47,025] [INFO] Target genome list was writen to GCF_022870865.1_ASM2287086v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:47,032] [INFO] Task started: fastANI
[2024-01-25 18:02:47,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg454b5f82-57bf-4eba-b86c-a519988e64e9/GCF_022870865.1_ASM2287086v1_genomic.fna.gz --refList GCF_022870865.1_ASM2287086v1_genomic.fna/target_genomes.txt --output GCF_022870865.1_ASM2287086v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:00,846] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:00,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf525099e-940c-478b-8608-d6af1fe294a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:00,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf525099e-940c-478b-8608-d6af1fe294a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:00,855] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:00,855] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:00,856] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	100.0	981	983	95	conclusive
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	82.8974	673	983	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	82.8842	634	983	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_014055005.1	194197	194197	type	True	80.6942	529	983	95	below_threshold
Neisseria dentiae	strain=NCTC13012	GCA_900453685.1	194197	194197	type	True	80.6283	550	983	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_002108595.1	194197	194197	type	True	80.4911	525	983	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	79.6249	450	983	95	below_threshold
Bergeriella denitrificans	strain=NCTC10295	GCA_900453875.1	494	494	type	True	79.5779	423	983	95	below_threshold
Bergeriella denitrificans	strain=NBRC 102155	GCA_001592185.1	494	494	type	True	79.4094	339	983	95	below_threshold
Neisseria elongata subsp. glycolytica	strain=NCTC11050	GCA_900475815.1	88719	495	type	True	78.7238	321	983	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	78.4334	340	983	95	below_threshold
Neisseria iguanae	strain=ATCC 51483	GCA_003013245.1	90242	90242	type	True	78.3913	319	983	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	78.3452	303	983	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:00,857] [INFO] DFAST Taxonomy check result was written to GCF_022870865.1_ASM2287086v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:00,857] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:00,858] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:00,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf525099e-940c-478b-8608-d6af1fe294a4/dqc_reference/checkm_data
[2024-01-25 18:03:00,858] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:00,890] [INFO] Task started: CheckM
[2024-01-25 18:03:00,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022870865.1_ASM2287086v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022870865.1_ASM2287086v1_genomic.fna/checkm_input GCF_022870865.1_ASM2287086v1_genomic.fna/checkm_result
[2024-01-25 18:03:31,644] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:31,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:31,659] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:31,659] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:31,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022870865.1_ASM2287086v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:31,660] [INFO] Task started: Blastn
[2024-01-25 18:03:31,660] [INFO] Running command: blastn -query GCF_022870865.1_ASM2287086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf525099e-940c-478b-8608-d6af1fe294a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_022870865.1_ASM2287086v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:32,987] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:32,990] [INFO] Selected 19 target genomes.
[2024-01-25 18:03:32,990] [INFO] Target genome list was writen to GCF_022870865.1_ASM2287086v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:33,009] [INFO] Task started: fastANI
[2024-01-25 18:03:33,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg454b5f82-57bf-4eba-b86c-a519988e64e9/GCF_022870865.1_ASM2287086v1_genomic.fna.gz --refList GCF_022870865.1_ASM2287086v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022870865.1_ASM2287086v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:44,513] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:44,525] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:03:44,525] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_004341385.1	s__Neisseria suis	82.9022	633	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.29	97.17	0.93	0.92	3	-
GCF_014055005.1	s__Neisseria dentiae	80.7826	524	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	-
GCF_900187305.1	s__Neisseria zoodegmatis	79.8355	442	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.30	96.60	0.95	0.90	3	-
GCF_900637855.1	s__Neisseria animaloris	79.783	415	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.11	0.97	0.94	5	-
GCF_014297595.1	s__Neisseria musculi	79.6338	479	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.59	0.96	0.96	3	-
GCF_002108505.1	s__Neisseria dumasiana	79.6141	433	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.54	97.26	0.91	0.89	4	-
GCF_001592185.1	s__Neisseria denitrificans	79.4057	339	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002216145.1	s__Neisseria chenwenguii	79.0064	418	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.73	99.73	0.96	0.96	2	-
GCF_009671065.1	s__Neisseria brasiliensis	79.0046	424	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.38	99.05	0.95	0.90	4	-
GCF_014898075.1	s__Neisseria sp011038745	78.9854	409	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.25	98.87	0.98	0.97	4	-
GCF_017753665.1	s__Neisseria sicca_D	78.7262	335	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.2415	96.44	95.35	0.92	0.88	6	-
GCF_000227275.1	s__Neisseria sp000227275	78.4934	329	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.3387	97.52	96.71	0.95	0.93	3	-
GCF_005221305.1	s__Neisseria subflava	78.4847	305	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.1594	96.50	96.31	0.91	0.87	10	-
GCF_003013245.1	s__Neisseria iguanae	78.4247	317	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901482445.1	s__Neisseria lactamica	78.3888	307	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.73	97.33	0.93	0.89	36	-
GCF_008807015.1	s__Neisseria zalophi	78.3402	301	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001809325.1	s__Neisseria sp001809325	78.2708	307	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCF_003044455.1	s__Neisseria bergeri	78.1704	293	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.18	96.14	0.94	0.92	5	-
GCF_001027865.1	s__Neisseria arctica	78.0506	310	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:44,529] [INFO] GTDB search result was written to GCF_022870865.1_ASM2287086v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:44,530] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:44,533] [INFO] DFAST_QC result json was written to GCF_022870865.1_ASM2287086v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:44,533] [INFO] DFAST_QC completed!
[2024-01-25 18:03:44,533] [INFO] Total running time: 0h1m9s